Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling

Abstract

Running title: DNA demixing and supercoiling.Abstract: This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to the formation of the nucleoid, which is the region of the cell that contains the genomic DNA in a rather compact form. Supercoiling describes the coiling of the axis of the DNA double helix to accommodate the torsional stress injected in the molecule by topoisomerases. Supercoiling is able to induce some compaction of the bacterial DNA, although to a lesser extent than demixing. In this paper, we investigate the interplay of these two mechanisms, with the goal of determining whether the total compaction ratio of the DNA is the mere sum or some more complex function of the compaction ratios due to each mechanism. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. This work reveals that there actually exist different regimes, depending on the crowder volume ratio and the DNA superhelical density. In particular, a regime where the effects of DNA demixing and supercoiling on the compaction of the DNA coil simply add up is shown to exist up to moderate values of the superhelical density. In contrast, the mean radius of the DNA coil no longer decreases above this threshold and may even increase again for sufficiently large crowder concentrations. Finally, the model predicts that the DNA coil may depart from the spherical geometry very close to the jamming threshold, as a trade-off between the need to minimize both the bending energy of the stiff plectonemes and the volume of the DNA coil to accommodate demixing.(#) marc.joyeux@univ-grenoble-alpes.fr Statement of significance: Many biological processes take place simultaneously in living cells. It is tempting to study each of them separately and rely on the hypothesis that cells behave like the "addition" of the isolated parts. This is however not always the case and the present work illustrates this fact. We consider two different processes, which are both able to compact the bacterial DNA, namely demixing and supercoiling, and we study how the DNA reacts when subject to both of them simultaneously. Through coarse-grained modeling and Brownian dynamics simulations, we show that the two processes are "additive" only in a limited range of biologically relevant values of the parameters and that their interplay is much more complex outside from this range.

Impact of Self-Association on the Architectural Properties of Bacterial Nucleoid Proteins

“…Concentrations of nucleotides and proteins are of the same order of magnitude as in vivo ones. For DNA, each bead represents 7.5 base pairs (bp) and the chain contains 2880 beads, equivalent to 21600 bp, as in (20,22,23). Each protein chain contains 7 beads with index m (1 7 m ≤ ≤ ), where terminal beads 1 m = and 7 represent the two DNA-binding sites of each protein, whereas beads 2 m = and 6 (for Model I) or 2 m = , 3, 5 and 6 (for Model II) represent the isomerization sites of the protein (Fig.…”

Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome

“…The coarse-grained bead-and-spring model developed for this study is described in detail in Supporting Materials and Methods , Model and Simulations. In brief, bacterial DNA is modeled, as in ( 30 , 36 ), as circular chains of n beads with a radius a = 10 nm separated at equilibrium by a distance l 0 = 2.5 nm, where two beads represent 15 DNA bp. Simulations were performed with unconstrained circular chains of length n = 600, equivalent to 4500 bp, which represent the plasmids used in ( 15 ).…”

“…As in ( 31 , 36 ), the torsional energy term was borrowed from ( 37 ) and requires the introduction of a body-fixed frame ( u k , f k , v k ), where u k denotes the unit vector pointing from bead k to bead k + 1. The torsional rigidity opposing rotation of ( u k , f k , v k ) around u k ( τ = 25 k B T ) was adjusted so that at equilibrium the writhe contribution accounts for ∼70% of the linking number difference ( 38 ), as is illustrated in Fig.…”

“…It may be worth emphasizing that introduction of the body-fixed frame ( u k , f k , v k ) is crucial for correctly modeling the torsion of double-stranded DNA with a “single-stranded” bead-and-spring model. This procedure is quite realistic and has already proved very useful for studying, for example, the interplay of DNA demixing and supercoiling in nucleoid compaction ( 36 ), the buckling transition in double-stranded DNA and RNA ( 39 ), the influence of nucleoid-associated proteins on DNA supercoiling ( 40 ), DNA supercoil relaxation ( 41 ), the competition between B-Z and B-L transitions in a single DNA molecule ( 42 ), the relaxation of DNA supercoils by topoisomerase IB ( 43 ), the sequence-dependent duplex denaturation in superhelical DNA ( 44 ), transcription-driven twin supercoiling of DNA loops ( 45 ), site juxtaposition in supercoiled DNA ( 46 ), and salt effects on the structure and internal dynamics of superhelical DNA ( 47 ).…”

“…To gain more detailed information on this mechanism, we determined the minimal physical properties that must be added to a standard model of circular DNA to reproduce the results described in ( 15 ). The starting model for this study was similar to those we proposed recently to investigate facilitated diffusion ( 25 , 26 , 27 ), the interactions of DNA and H-NS nucleoid proteins ( 28 , 29 , 30 ), the formation of the bacterial nucleoid ( 31 , 32 , 33 , 34 , 35 ), and the interplay of DNA demixing and supercoiling in compacting the nucleoid ( 36 ).…”